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Di Rocco G, Battistuzzi G, Borsari M, Bortolotti CA, Ranieri A, Sola M. The enthalpic and entropic terms of the reduction potential of metalloproteins: Determinants and interplay. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214071] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Zanello P. The competition between chemistry and biology in assembling iron–sulfur derivatives. Molecular structures and electrochemistry. Part I. {Fe(SγCys)4} proteins. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2013.02.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Caranto JD, Gebhardt LL, MacGowan CE, Limberger RJ, Kurtz DM. Treponema denticola superoxide reductase: in vivo role, in vitro reactivities, and a novel [Fe(Cys)(4)] site. Biochemistry 2012; 51:5601-10. [PMID: 22715932 DOI: 10.1021/bi300667s] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
In vitro and in vivo results are presented demonstrating that superoxide reductase (SOR) from the air-sensitive oral spirochete, Treponema denticola (Td), is a principal enzymatic scavenger of superoxide in this organism. This SOR contains the characteristic non-heme [Fe(His)(4)Cys] active sites. No other metal-binding domain has been annotated for Td SOR. However, we found that Td SOR also accommodates a [Fe(Cys)(4)] site whose spectroscopic and redox properties resemble those in so-called 2Fe-SORs. Spectroscopic comparisons of the wild type and engineered Cys → Ser variants indicate that three of the Cys ligands correspond to those in [Fe(Cys)(4)] sites of "canonical" 2Fe-SORs, whereas the fourth Cys ligand residue has no counterpart in canonical 2Fe-SORs or in any other known [Fe(Cys)(4)] protein. Structural modeling is consistent with iron ligation of the "noncanonical" Cys residue across subunit interfaces of the Td SOR homodimer. The Td SOR was isolated with only a small percentage of [Fe(Cys)(4)] sites. However, quantitative formation of stable [Fe(Cys)(4)] sites was readily achieved by exposing the as-isolated protein to an iron salt, a disulfide reducing agent and air. The disulfide/dithiol status and iron occupancy of the Td SOR [Fe(Cys)(4)] sites could, thus, reflect intracellular redox status, particularly during periods of oxidative stress.
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Affiliation(s)
- Jonathan D Caranto
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX 78249, USA
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Sun N, Dey A, Xiao Z, Wedd AG, Hodgson KO, Hedman B, Solomon EI. Solvation effects on S K-edge XAS spectra of Fe-S proteins: normal and inverse effects on WT and mutant rubredoxin. J Am Chem Soc 2011; 132:12639-47. [PMID: 20726554 DOI: 10.1021/ja102807x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
S K-edge X-ray absorption spectroscopy (XAS) was performed on wild type Cp rubredoxin and its Cys --> Ser mutants in both solution and lyophilized forms. For wild type rubredoxin and for the mutants where an interior cysteine residue (C6 or C39) is substituted by serine, a normal solvent effect is observed, that is, the S covalency increases upon lyophilization. For the mutants where a solvent accessible surface cysteine residue is substituted by serine, the S covalency decreases upon lyophilization which is an inverse solvent effect. Density functional theory (DFT) calculations reproduce these experimental results and show that the normal solvent effect reflects the covalency decrease due to solvent H-bonding to the surface thiolates and that the inverse solvent effect results from the covalency compensation from the interior thiolates. With respect to the Cys --> Ser substitution, the S covalency decreases. Calculations indicate that the stronger bonding interaction of the alkoxide with the Fe relative to that of thiolate increases the energy of the Fe d orbitals and reduces their bonding interaction with the remaining cysteines. The solvent effects support a surface solvent tuning contribution to electron transfer, and the Cys --> Ser result provides an explanation for the change in properties of related iron-sulfur sites with this mutation.
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Affiliation(s)
- Ning Sun
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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Morleo A, Bonomi F, Iametti S, Huang VW, Kurtz DM. Iron-nucleated folding of a metalloprotein in high urea: resolution of metal binding and protein folding events. Biochemistry 2010; 49:6627-34. [PMID: 20614892 DOI: 10.1021/bi100630t] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Addition of iron salts to chaotrope-denatured aporubredoxin (apoRd) leads to nearly quantitative recovery of its single Fe(SCys)(4) site and native protein structure without significant dilution of the chaotrope. This "high-chaotrope" approach was used to examine iron binding and protein folding events using stopped-flow UV-vis absorption and CD spectroscopies. With a 100-fold molar excess of ferrous iron over denatured apoRd maintained in 5 M urea, the folded holoFe(III)Rd structure was recovered in >90% yield with a t(1/2) of <10 ms. More modest excesses of iron also gave nearly quantitative holoRd formation in 5 M urea but with chronological resolution of iron binding and protein folding events. The results indicate structural recovery in 5 M urea consists of the minimal sequence: (1) binding of ferrous iron to the unfolded apoRd, (2) rapid formation of a near-native ferrous Fe(SCys)(4) site within a protein having no detectable secondary structure, and (3) recovery of the ferrous Fe(SCys)(4) site chiral environment nearly concomitantly with (4) recovery of the native protein secondary structure. The rate of step 2 (and, by inference, step 1) was not saturated even at a 100-fold molar excess of iron. Analogous results obtained for Cys --> Ser iron ligand variants support formation of an unfolded-Fe(SCys)(3) complex between steps 1 and 2, which we propose is the key nucleation event that pulls together distal regions of the protein chain. These results show that folding of chaotrope-denatured apoRd is iron-nucleated and driven by extraordinarily rapid formation of the Fe(SCys)(4) site from an essentially random coil apoprotein. This high-chaotrope, multispectroscopy approach could clarify folding pathways of other [M(SCys)(3)]- or [M(SCys)(4)]-containing proteins.
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Affiliation(s)
- Anna Morleo
- DISMA, University of Milan, Via G. Celoria 2, 20133 Milan, Italy
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Xiao Z, Donnelly PS, Zimmermann M, Wedd AG. Transfer of Copper between Bis(thiosemicarbazone) Ligands and Intracellular Copper-Binding Proteins. Insights into Mechanisms of Copper Uptake and Hypoxia Selectivity. Inorg Chem 2008; 47:4338-47. [DOI: 10.1021/ic702440e] [Citation(s) in RCA: 155] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Zhiguang Xiao
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Paul S. Donnelly
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Matthias Zimmermann
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Anthony G. Wedd
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, University of Melbourne, Parkville, Victoria 3010, Australia
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Baran P, Boca R, Chakraborty I, Giapintzakis J, Herchel R, Huang Q, McGrady JE, Raptis RG, Sanakis YO, Simopouloso A. Synthesis, characterization, and study of octanuclear iron-oxo clusters containing a redox-active Fe4O4-cubane core. Inorg Chem 2007; 47:645-55. [PMID: 18078337 DOI: 10.1021/ic7020337] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A one-pot synthetic procedure yields the octanuclear Fe(III) complexes Fe(8)(micro(4-)O)(4)(micro-pz(*))(12)X(40, where X = Cl and pz(*) = pyrazolate anion (pz = C(3)H(3)N(2)-) (1), 4-Cl-pz (2), and 4-Me-pz (3) or X = Br and pz(*) = pz (4). The crystal structures of complexes 1-4, determined by X-ray diffraction, show an Fe(4)O(4)-cubane core encapsulated in a shell composed of four interwoven Fe(micro-pz(*))(3)X units. Complexes 1-4 have been characterized by 1H NMR, infrared, and Raman spectroscopies. Mössbauer spectroscopic analysis distinguishes the cubane and outer Fe(III) centers by their different isomer shift and quadrupole splitting values. Electrochemical analyses by cyclic voltammetry show four consecutive, closely spaced, reversible reduction processes for each of the four complexes. Magnetic susceptibility studies, corroborated by density functional theory calculations, reveal weak antiferromagnetic coupling among the four cubane Fe centers and strong antiferromagnetic coupling between cubane and outer Fe atoms of 1. The structural similarity between the antiferromagnetic Fe(8)(micro(4-)O)(4) core of 1-4 and the antiferromagnetic units contained in the minerals ferrihydrite and maghemite is demonstrated by X-ray and Mössbauer data.
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Affiliation(s)
- Peter Baran
- Department of Chemistry and the Institute of Functional Nanomaterials, University of Puerto Rico, San Juan, Puerto Rico 00931-3346, USA
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Walker FA. The heme environment of mouse neuroglobin: histidine imidazole plane orientations obtained from solution NMR and EPR spectroscopy as compared with X-ray crystallography. J Biol Inorg Chem 2006; 11:391-7. [PMID: 16586113 DOI: 10.1007/s00775-006-0095-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2006] [Accepted: 02/22/2006] [Indexed: 12/16/2022]
Abstract
The 1H NMR chemical shifts of the heme methyl groups of the ferriheme complex of metneuroglobin (Du et al. in J. Am. Chem. Soc. 125:8080-8081, 2003) predict orientations of the axial histidine ligands (Shokhirev and Walker in J. Biol. Inorg. Chem. 3:581-594, 1998) that are not consistent with the X-ray data (Vallone et al. in Proteins Struct. Funct. Bioinf. 56:85-94, 2004), and the EPR spectrum (Vinck et al. in J. Am. Chem. Soc. 126:4516-4517, 2004) is only marginally consistent with these data. The reasons for these inconsistencies appear to be rooted in the high degree of aqueous solution exposure of the heme group and the fact that there are no strong hydrogen-bond acceptors for the histidine imidazole N-H protons provided by the protein. Similar inconsistencies may exist for other water-soluble heme proteins, and 1H NMR spectroscopy provides a simple means to verify whether the solution structure of the heme center is the same as or different from that in the crystalline state.
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Affiliation(s)
- F Ann Walker
- Department of Chemistry, The University of Arizona, PO Box 210041, Tucson, AZ 85721-0041, USA.
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Sundararajan M, Hillier IH, Burton NA. Structure and Redox Properties of the Protein, Rubredoxin, and Its Ligand and Metal Mutants Studied by Electronic Structure Calculation. J Phys Chem A 2005; 110:785-90. [PMID: 16405354 DOI: 10.1021/jp054276a] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The changes in the structural and electronic properties accompanying metal ionization of the iron-containing protein, rubredoxin, and of some ligand and metal mutants, have been explored using density functional theory (DFT) calculations of the metal atom coordinated to the four immediate residues. Both isolated and embedded cluster studies have been carried out, the latter using the hybrid quantum mechanics/molecular mechanics (QM/MM) approach. The replacement of a cysteine by a serine residue has a considerable effect on both the electronic and geometric structure of the core, which can be qualitatively understood on the basis of the isolated cluster studies. The modulation of these properties caused by the protein environment is quite accurately described by the QM/MM calculations. The predicted core geometries are in good accord with both X-ray and EXAFS data, and the changes in the redox potentials are predicted, at least semiquantitatively, by considering only the core part of the protein.
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Auchère F, Sikkink R, Cordas C, Raleiras P, Tavares P, Moura I, Moura JJG. Overexpression and purification of Treponema pallidum rubredoxin; kinetic evidence for a superoxide-mediated electron transfer with the superoxide reductase neelaredoxin. J Biol Inorg Chem 2004; 9:839-49. [PMID: 15328557 DOI: 10.1007/s00775-004-0584-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2004] [Accepted: 07/22/2004] [Indexed: 10/26/2022]
Abstract
Superoxide reductases are a class of non-haem iron enzymes which catalyse the monovalent reduction of the superoxide anion O2- into hydrogen peroxide and water. Treponema pallidum (Tp), the syphilis spirochete, expresses the gene for a superoxide reductase called neelaredoxin, having the iron protein rubredoxin as the putative electron donor necessary to complete the catalytic cycle. In this work, we present the first cloning, overexpression in Escherichia coli and purification of the Tp rubredoxin. Spectroscopic characterization of this 6 kDa protein allowed us to calculate the molar absorption coefficient of the 490 nm feature of ferric iron, epsilon=6.9+/-0.4 mM(-1) cm(-1). Moreover, the midpoint potential of Tp rubredoxin, determined using a glassy carbon electrode, was -76+/-5 mV. Reduced rubredoxin can be efficiently reoxidized upon addition of Na(2)IrCl(6)-oxidized neelaredoxin, in agreement with a direct electron transfer between the two proteins, with a stoichiometry of the electron transfer reaction of one molecule of oxidized rubredoxin per one molecule of neelaredoxin. In addition, in presence of a steady-state concentration of superoxide anion, the physiological substrate of neelaredoxin, reoxidation of rubredoxin was also observed in presence of catalytic amounts of superoxide reductase, and the rate of rubredoxin reoxidation was shown to be proportional to the concentration of neelaredoxin, in agreement with a bimolecular reaction, with a calculated k(app)=180 min(-1). Interestingly, similar experiments performed with a rubredoxin from the sulfate-reducing bacteria Desulfovibrio vulgaris resulted in a much lower value of k(app)=4.5 min(-1). Altogether, these results demonstrated the existence for a superoxide-mediated electron transfer between rubredoxin and neelaredoxin and confirmed the physiological character of this electron transfer reaction.
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Affiliation(s)
- Françoise Auchère
- REQUIMTE-Centro de Química Fina e Biotecnologia, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
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Bertini I, Luchinat C, Nerinovski K, Parigi G, Cross M, Xiao Z, Wedd AG. Application of NMRD to hydration of rubredoxin and a variant containing a (Cys-S)3FeIII(OH) site. Biophys J 2003; 84:545-51. [PMID: 12524306 PMCID: PMC1302634 DOI: 10.1016/s0006-3495(03)74873-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Hydration of oxidized rubredoxin (Fe(III)(S-Cys)(4) center) was investigated by (1)H and (17)O relaxation measurements of bulk water as a function of the applied magnetic field (nuclear magnetic relaxation dispersion). Oxidized rubredoxin showed an increased water (1)H relaxation profile with respect to the diamagnetic gallium derivative or reduced species. Analysis of the data shows evidence of exchangeable proton(s) approximately 4.0-4.5 A from the metal ion, the exchange time being longer than 10(-10) s and shorter than 10(-5) s. The correlation time for the proton-electrons interaction is 7 x 10(-11) s and is attributed to the effective electron relaxation time. Its magnitude is consistent with the large signal linewidths of the protein donor nuclei, observed in high resolution NMR spectra. For reduced rubredoxin, such correlation time is proposed to be smaller than 10(-11) s. (17)O relaxation measurements suggest the presence of at least one long-lived protein-bound water molecule. Analogous relaxation measurements were performed on the C6S rubredoxin variant, whose iron(III) center has been previously shown to be coordinated to three cysteine residues and a hydroxide ion above pH 6. (1)H nuclear magnetic relaxation dispersion profiles indicate increased hydration with respect to the wild-type.
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Affiliation(s)
- Ivano Bertini
- CERM and Department of Chemistry, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy.
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